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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: give each electrocardiogram (ECG) the plasma concentration
measured closest in time to it, before or after: the sample's sequence
number (PCSEQ), date/time (PCDTM) and concentration (PCCONC), and the
hours between the sample and the ECG (PCDIST).
Input: one spec.yaml over ECG records, each with its sequence number
(EGSEQ) and its date and time, and pharmacokinetic (PK) concentration
records, each with its sequence number, collected date/time text and
result.
Variables:
ADTM: the ECG date and time; empty when none was recorded.PCSEQ: the sequence number of the subject's sample closest in time to the ECG; empty when no eligible sample exists. Of two samples equally close, the one taken before the ECG is chosen, whatever their sequence numbers; of two taken at the same time, the one with the lower sequence number.PCDTM: the date and time of that selected sample; empty when no eligible sample exists.PCCONC: the concentration of that selected sample; empty when no eligible sample exists.PCDIST: hours betweenPCDTMandADTM, without direction and not rounded.
Note: an hour distance needs a clock time on both sides. A sample whose time was not recorded to the minute, such as one recorded with a date alone, is never chosen, instead of being placed at midnight, and an ECG with no date and time is paired with no sample. Its four sample columns are then empty, as they are when no sample of the subject has such a time.
Inputs
Under review2 source filesinput/eg.csv
Edit4 rows| STUDYID | USUBJID | EGSEQ | EGDTC |
|---|---|---|---|
| YAMAA-01 | 1 | 2024-03-10T06:30 | |
| YAMAA-01 | 2 | — | |
| YAMAA-01 | 1 | 2024-03-10T12:00 | |
| YAMAA-01 | 2 | 2024-03-10T13:30 |
input/pc.csv
Edit6 rows| STUDYID | USUBJID | PCSEQ | PCDTC | PCSTRESN |
|---|---|---|---|---|
| YAMAA-01 | 1 | 2024-03-09T22:00 | 12.4 | |
| YAMAA-01 | 2 | 2024-03-10 | 15.8 | |
| YAMAA-01 | 3 | 2024-03-10T13:15 | 48.3 | |
| YAMAA-01 | 1 | 2024-03-10T13:00 | 25.6 | |
| YAMAA-01 | 3 | 2024-03-10T11:00 | 29.7 | |
| YAMAA-01 | 2 | 2024-03-10T11:00 | 30.2 |
Expected output
Under review4 expected rowsexpected/adeg.csv
Edit4 rows| STUDYID | USUBJID | EGSEQ | ADTM | PCSEQ | PCDTM | PCCONC | PCDIST |
|---|---|---|---|---|---|---|---|
| YAMAA-01 | 1 | 2024-03-10T06:30:00 | 3 | 2024-03-10T13:15:00 | 48.3 | 6.75 | |
| YAMAA-01 | 2 | — | — | — | — | — | |
| YAMAA-01 | 1 | 2024-03-10T12:00:00 | 2 | 2024-03-10T11:00:00 | 30.2 | 1 | |
| YAMAA-01 | 2 | 2024-03-10T13:30:00 | 1 | 2024-03-10T13:00:00 | 25.6 | 0.5 |
Human review and assessment
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADEG | STUDYID | Study Identifier | character | Copy value from EG.STUDYID. | Predecessor | ||
| ADEG | USUBJID | Unique Subject Identifier | character | Copy value from EG.USUBJID. | Predecessor | ||
| ADEG | EGSEQ | Sequence Number | numeric | Copy value from EG.EGSEQ. | Predecessor | ||
| ADEG | ADTM | Analysis Date/Time | numeric | ISO 8601 | Copy value from EG.EGDTC. | Predecessor | |
| ADEG | PCSEQ | Sequence Number of the Closest Sample | numeric | Take PCSEQ from the first PC record matching on STUDYID and USUBJID, where PC.DIST IS NOT NULL AND PC.PREC IN ('minute', 'second'), ordered by PC.DIST then PC.GAP descending then PC.PCSEQ, and no match yields blank. | Derived | ||
| ADEG | PCDTM | Date/Time of the Closest Sample | numeric | ISO 8601 | Take PCDTM from the first PC record matching on STUDYID and USUBJID, where PC.DIST IS NOT NULL AND PC.PREC IN ('minute', 'second'), ordered by PC.DIST then PC.GAP descending then PC.PCSEQ, where PCDTM is derived as impute incomplete datetime from PCDTC, giving each time part the source lacks its earliest value; a source without a complete date gives blank; invalid text is an error, and no match yields blank. | Derived | |
| ADEG | PCCONC | Concentration of the Closest Sample | numeric | Take PCSTRESN from the first PC record matching on STUDYID and USUBJID, where PC.DIST IS NOT NULL AND PC.PREC IN ('minute', 'second'), ordered by PC.DIST then PC.GAP descending then PC.PCSEQ, and no match yields blank. | Derived | ||
| ADEG | PCDIST | Hours Between Closest Sample and ECG | numeric | Take DIST from the first PC record matching on STUDYID and USUBJID, where PC.DIST IS NOT NULL AND PC.PREC IN ('minute', 'second'), ordered by PC.DIST then PC.GAP descending then PC.PCSEQ, where DIST is derived as compute ABS(GAP), and no match yields blank. | Derived |
| Version | Date | Author | Description | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 1.7 | 2026-10-20 | yamaa docs build | Read a specification in the 1.0 surface as its 0.5 counterpart; state that missing values stay missing where a mapping declares no missing handler, and leave out a declared missing answer that restates a handler's default | ||
| 1.6 | 2026-10-17 | yamaa docs build | Describe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight | ||
| 1.5 | 2026-10-17 | yamaa docs build | Name collected precision in words instead of letter codes; state imputation fallbacks, minimum source precision, bounds ignored outside the collected period, and invalid text with no handler as an error; describe date and datetime shifts, imputation flag codes, and partial text giving no date part | ||
| 1.4 | 2026-10-15 | yamaa docs build | State datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks | ||
| 1.3 | 2026-09-29 | yamaa docs build | Show study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata | ||
| 1.2 | 2026-09-29 | yamaa docs build | Classify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived | ||
| 1.1 | 2026-09-29 | yamaa docs build | Resolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML | ||
| 1.0 | yamaa docs build | Initial generation from spec.yaml |